\documentclass{article}
\title{Sweave Example}
\author{Kate Cowles}
\usepackage{Sweave}
\begin{document}
\maketitle


The {\tt Sweave} function facilitates creation of documents 
that blend R code, its output, and documentation or other text.  
The user begins by creating a {\tt noweb} source file, which is 
a text file with the extension {\tt .Rnw}.  It resembles a 
{\tt .tex} file, but it has two kinds of segments (called 
``chunks") in it:  \emph{documentation chunks} and 
\emph{code chunks}.  By default, the document begins with a 
documentation chunk.  Each code chunk must start with 
\begin{verbatim}
 <<>>=
\end{verbatim} 
at the beginning of a line.  Optionally, a name for the code 
chunk may be included in the angle brackets:
\begin{verbatim}
 <<name>>=
\end{verbatim}
Code chunk names may be used to pass options to Sweave to 
control the final output.

Each documentation chunk (except the first) begins with
\begin{verbatim}
  @
\end{verbatim}
at the beginning of a line.   
  

In this example, we create a small data frame, run a linear 
regression model, and produce diagnostic plots.  Since we do not 
specify any options in a code chunk name, the default behavior 
occurs:  both the code and its output are included in the final 
document.

<<>>=
set.seed(15)
x <- 1:5
y <- rnorm(1 -0.5* x )
mydat <- data.frame(cbind(x,y))
print(mydat)
summary( lmout <- lm( y ~ x, data=mydat) )
@

Next we will create plots.  The options {\tt fig} and {\tt echo} 
in the code chunk name tell Sweave to include the actual
plots produced, and to suppress printing (echoing) of the R code.

\begin{center}
<<fig=TRUE,echo=FALSE>>=
par(mfrow=c(2,2))
plot(lmout)
@
\end{center}

This time we will show the code that produces the figure, instead 
of the figure itself.

\begin{center}
<<fig=FALSE, echo=TRUE>>=
par(mfrow=c(2,2))
plot(lmout)
@
\end{center}

It is also possible to include the scalar results of R 
expressions in text chunks. For example, the logit of 0.237 is
\Sexpr{ log( 0.237/( 1-0.237)) }. 

Emacs has special facilities for processing .Rnw files.  Bring up emacs,
and use {\tt File/New frame} to open a second frame.  In one of the two
frames, enter {\tt Alt-X R} to bring up R.  In the other frame, either open
an existing .Rnw file, or create a new file with the extension {\tt .Rnw}.
This causes the \LaTeX\ -related icons to appear, as well as a menu tab
called {\tt Noweb}.  When you are ready to process your .Rnw file in R, choose
the {\tt Noweb} tab, then {\tt Sweave}, then {\tt Sweave}.  After that has
worked without errors, so that the {\tt .tex} file has been created, choose
{\tt Noweb}, {\tt Sweave}, {\tt PDF(Latex)}.

Alternatively, one may do the following step-by-step process.
First,  create the .Rnw file in a text editor.  
Then go into R and run the Sweave 
function.
\begin{verbatim}
Sweave(file="firsttry.Rnw")
\end{verbatim}

%\begin{verbatim}
%cho 'Sweave("firsttry.Rnw")' | R --vanilla --quiet
%\end{verbatim}
%at the Linux/Unix prompt without having to go into R.

Either way of running the {\tt Sweave} function will create the 
\LaTeX\ source file {\tt firsttry2012.tex} and the graphics files 
{\tt firsttry2012-002.pdf} and {\tt firsttry2012-002.ps}.  The final 
typeset document may be produced by running
\begin{verbatim}
pdflatex firsttry2012
\end{verbatim}
at the Linux/Unix prompt.  If in Windows, a batch file or the 
TeXnic Center may be used to process the {\tt .tex} file.

Note that \LaTeX\ must be able to locate the Sweave style file
on your system for this to work.  

\end{document}